[Chimera-users] How to select residues/atoms only those within my cryo-EM map region

[Elaine Meng]

Hi Doonam,
You can assign the local density values to atoms and then select only those atoms with values greater than some threshold.

(1)  Assign density values as atom attributes.  menu: Tools…Volume Data… Values at Atom Positions.  In that dialog choose atomic model and map model, then click Histogram.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/density/density.html>

(2) … which will show the Render/Select by Attribute tool with a histogram of the values assigned to the atoms.  It is showing the Render tab, in which you could color the atoms by the density values if you wanted to.  To select only a subset of atoms by those values, first look at the attribute name in the Render tab, then change to the Select tab, choose that same attribute, and then move the vertical bars on the histogram to select the atoms you want (presumably the higher-value range), click Apply.

You can do this all with commands.  Part (1) above  can be done with command “measure mapValues” in which you can also specify a name for the new attribute.  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#mapValues>
Part (2) can be done directly with the “select” command.  For example, if I’d named the new attribute “mapd” then you could use a command something like: 

select @/mapd>0.085

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/select.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descriptors>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On May 4, 2019, at 10:20 PM, Kim, Doo Nam <doonam at lanl.gov> wrote:
>  
> Dear all,
> I want to select residues/atoms only those within my cryo-EM map region so that I can highlight/color them.
> 
> As I googled ("select atoms only within a map chimera"), I could find only how to select residues/atoms within certain radius from specific position/atoms.
> 
> I may use phenix.map_model_cc to see which residues have higher cc to my cryo-EM map and manually select those using a script.
> 
> However, I'm just curious whether there is already a good automatic chimera function that I can use to select residues/atoms only those within my cryo-EM map region.
> best,
> Doonam